Currently, there are no practical ways to measure sequence (e.g., gene) copy number accurately, especially for high copy numbers, as part of a plant breeding program or other mass analysis. Some assays exist, such as whole-genome sequencing and fiber-FISH (Fluorescence In-Situ Hybridization); however these are impractically slow and expensive to apply to hundreds or thousands of samples for the purpose of measuring copy number. Quantitative PCR methods tend to be inaccurate and require very high quality DNA (such as high quality genomic DNA) as starting material, which is difficult and expensive to obtain. The existing TAQMAN® PCR Copy Number assay requires a separate control locus reaction to ensure accuracy which doubles costs and leads to inaccuracy caused by differential amplification of the different control and target sequences, making it expensive and impractical for large numbers of plants or high copy number loci.